jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
lammps/doc/fix_reax_bonds.html

249 lines
9.8 KiB
HTML
Raw Normal View History

'' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13800 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-30 22:53:28 +08:00
<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14391 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-12-20 02:42:24 +08:00
<title>fix reax/bonds command &mdash; LAMMPS 17 Dec 2015 documentation</title>
'' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13800 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-30 22:53:28 +08:00
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14391 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-12-20 02:42:24 +08:00
<link rel="top" title="LAMMPS 17 Dec 2015 documentation" href="index.html"/>
'' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13800 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-30 22:53:28 +08:00
<script src="_static/js/modernizr.min.js"></script>
</head>
<body class="wy-body-for-nav" role="document">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="Manual.html" class="icon icon-home"> LAMMPS
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
&nbsp;
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="Manual.html">LAMMPS</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>fix reax/bonds command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Website</a>
<a href="Section_commands.html#comm">Commands</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="fix-reax-bonds-command">
<span id="index-0"></span><h1>fix reax/bonds command<a class="headerlink" href="#fix-reax-bonds-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="fix-reax-c-bonds-command">
<h1>fix reax/c/bonds command<a class="headerlink" href="#fix-reax-c-bonds-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID reax/bonds Nevery filename
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>reax/bonds = style name of this fix command</li>
<li>Nevery = output interval in timesteps</li>
<li>filename = name of output file</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix 1 all reax/bonds 100 bonds.tatb
fix 1 all reax/c/bonds 100 bonds.reaxc
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Write out the bond information computed by the ReaxFF potential
specified by <a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a> or <a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a> in the exact same format as the original
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9899 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2013-05-24 02:01:56 +08:00
stand-alone ReaxFF code of Adri van Duin. The bond information is
'' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13800 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-30 22:53:28 +08:00
written to <em>filename</em> on timesteps that are multiples of <em>Nevery</em>,
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9899 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2013-05-24 02:01:56 +08:00
including timestep 0. For time-averaged chemical species analysis,
'' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13800 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-30 22:53:28 +08:00
please see the <code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">species</span></code> command.</p>
<p>The format of the output file should be self-explantory.</p>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline"></a></h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3949 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2010-04-03 00:51:06 +08:00
are relevant to this fix. No global or per-atom quantities are stored
'' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13800 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-30 22:53:28 +08:00
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. No parameter of this fix can
be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a> command.
This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The fix reax/bonds command requires that the <a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a> be invoked. This fix is part of the REAX
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8056 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2012-05-14 23:52:01 +08:00
package. It is only enabled if LAMMPS was built with that package,
which also requires the REAX library be built and linked with LAMMPS.
'' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13800 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-30 22:53:28 +08:00
The fix reax/c/bonds command requires that the <a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a> be invoked. This fix is part of the
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9899 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2013-05-24 02:01:56 +08:00
USER-REAXC package. It is only enabled if LAMMPS was built with that
'' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13800 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-30 22:53:28 +08:00
package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a>, <a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a>, <a class="reference internal" href="fix_reaxc_species.html"><em>fix reax/c/species</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14349 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-12-11 01:23:56 +08:00
&copy; Copyright 2013 Sandia Corporation.
'' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13800 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-30 22:53:28 +08:00
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14391 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-12-20 02:42:24 +08:00
VERSION:'17 Dec 2015',
'' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13800 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-30 22:53:28 +08:00
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.StickyNav.enable();
});
</script>
</body>
</html>